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At least 253 records · Page 14Linked to original sources
PubMed2003

Automated protein NMR resonance assignments.

NMR resonance peak assignment is one of the key steps in solving an NMR protein structure. The assignment process links resonance peaks to individual residues of the target protein sequence, providing the prerequisite for establishing intra- and inter-residue spatial relationships between atoms. The assignment process is tedious and time-consuming, which could take many weeks. Though there exist a number of computer programs to assist the assignment process, many NMR labs are still doing the assignments manually to ensure quality. This paper presents (1) a new scoring system for mapping spin systems to residues, (2) an automated adjacency information extraction procedure from NMR spectra, and (3) a very fast assignment algorithm based on our previous proposed greedy filtering method and a maximum matching algorithm to automate the assignment process. The computational tests on 70 instances of (pseudo) experimental NMR data of 14 proteins demonstrate that the new score scheme has much better discerning power with the aid of adjacency information between spin systems simulated across various NMR spectra. Typically, with automated extraction of adjacency information, our method achieves nearly complete assignments for most of the proteins. The experiment shows very promising perspective that the fast automated assignment algorithm together with the new score scheme and automated adjacency extraction may be ready for practical use.

Algorithms↗
PubMed1999

Nutrition in the management of acquired immunodeficiency syndrome.

OBJECTIVE: To highlight the influence of nutrition on the progress of HIV/AIDS and the role and importance of good nutrition in the management of the disease. STUDY SELECTION: The subject was selected because it is now recognised that nutritional care and support is an essential component of the health care plan and management for people with HIV/AIDS. The subject is especially relevant since few studies have been conducted locally on the effects of nutritional status on the progression of HIV/AIDS. DATA RESOURCES AND DATA SYNTHESIS: A review of current literature selected from local and international scientific journals and books on the subject of nutrition and HIV/AIDS. DATA EXTRACTION AND SYNTHESIS: Data were developed from the reviewed information extracted from the contribution of different authors who are interested in nutritional management of people with HIV/AIDS. It was then analysed and synthesised into the current article. CONCLUSION: On the basis of the reviewed information, it is recommended that individuals with HIV/AIDS be given nutrition counselling and support to enable them achieve an adequate nutrient and energy intake for as long as possible. This would enhance the quality of their lives and minimise disease symptoms.

Acquired Immunodeficiency Syndrome↗
PubMed2000

Automatic extraction of protein interactions from scientific abstracts.

This paper motivates the use of Information Extraction (IE) for gathering data on protein interactions, describes the customization of an existing IE system, SRI's Highlight, for this task and presents the results of an experiment on unseen Medline abstracts which show that customization to a new domain can be fast, reliable and cost-effective.

Abstracting and Indexing↗
PubMed2005

Enhancing the sensitivity of fluorescence correlation spectroscopy by using time-correlated single photon counting.

Fluorescence correlation spectroscopy (FCS) and fluorescence cross-correlation spectroscopy (FCCS) are methods that extract information about a sample from the influence of thermodynamic equilibrium fluctuations on the fluorescence intensity. This method allows dynamic information to be obtained from steady state equilibrium measurements and its popularity has dramatically increased in the last 10 years due to the development of high sensitivity detectors and its combination with confocal microscopy. Using time-correlated single-photon counting (TCSPC) detection and pulsed excitation, information over the duration of the excited state can be extracted and incorporated in the analysis. In this short review, we discuss new methodologies that have recently emerged which incorporated fluorescence lifetime information or TCSPC data in the FCS and FCCS analysis. Time-gated FCS discriminates between which photons are to be incorporated in the analysis dependent upon their arrival time after excitation. This allows for accurate FCS measurements in the presence of fluorescent background, determination of sample homogeneity, and the ability to distinguish between static and dynamic heterogeneities. A similar method, time-resolved FCS can be used to resolve the individual correlation functions from multiple fluorophores through the different fluorescence lifetimes. Pulsed interleaved excitation (PIE) encodes the excitation source into the TCSPC data. PIE can be used to perform dual-channel FCCS with a single detector and allows elimination of spectral cross-talk with dual-channel detection. For samples that undergo fluorescence resonance energy transfer (FRET), quantitative FCCS measurements can be performed in spite of the FRET and the static FRET efficiency can be determined.

Algorithms↗
PubMed2005

Analysis of local orientation gradients in deformed single crystals.

Grain fragmentation and local orientation gradients in deformed single crystals are characterized using electron backscatter diffraction (EBSD) to obtain statistically reliable information. Interrogation of the dislocation substructure is accomplished by extracting information gleaned from small point-to-point misorientations as measured by EBSD. Along with an estimate of the geometrically necessary dislocation (GND) content, the point-to-point deviation from an average grain orientation is described by an orientation difference vector defined in Rodrigues space. Mapping of parameters such as GND, and divergence and gradient fields created from analysis of the difference vectors provide an alternative approach to obtain quantitative information and images from EBSD data.

Journal Article↗
PubMed2003

Rotational resonance NMR: separation of dipolar coupling and zero quantum relaxation.

The solid state NMR technique of rotational resonance (R2) has been used extensively to measure distances approaching 5-6 A between 13C nuclei in a variety of compounds including amyloidogenic peptides and membrane proteins. The accuracy of the distance information extracted from the time-dependent spin dynamics at R2 is often limited by the accuracy with which the relevant zero-quantum lineshape parameters are estimated. Here we demonstrate that measurement of spinning frequency dependent magnetization exchange dynamics provides data from which both distance and zero-quantum relaxation parameters can be extracted independently. In addition to providing more accurate distance information, this technique allows examination of the zero-quantum lineshape, which can indicate the presence of correlated relaxation or chemical shift distributions between dipolar-coupled sites. With this approach we have separated the contribution of dipolar couplings and zero quantum relaxation to R2 exchange curves. Thus, we have significantly improved the accuracy of the measurement of the intramolecular, internuclear distances between a pair of 13C's in two model compounds (N-acetyl-D,L-valine and glycylglycine.HCl) that lie in the distance range 4.6-4.7 A.

Carbon Isotopes↗
PubMed2005

Optimum information in crackling noise.

The crackling noise due to scratching superhard nanocomposite coatings was investigated by using a simple stick-slip model. The optimum information extracted from statistical analysis, in terms of the Akaike information criterion, is in good agreement with real tests. As a nanocomposite coating approaches an optimal performance, the acoustic emission energy follows a power-law distribution and its behavior is likely to be independent of microscopic and macroscopic details. The results imply that a peculiar deformation behavior, due to the competition between different deformation mechanisms such as dislocation pile-ups in nanocrystalline grains and grain sliding-grain rotation within amorphous boundaries, plays a vital role in the nanostructure with superhardness.

Journal Article↗
PubMed1986

Importance of global information in vernier acuity.

Noisy vernier configurations were generated by normally distributing the lateral displacements of dot elements forming vertical dotted lines. Observations with noisy configurations were compared with thresholds obtained with noise-free lines. In configurations with gap, we have found, through independent perturbation of the end regions adjacent to the gap, that the entire length of the line was actively processed. In an experiment with noisy abutting lines, the threshold as a function of line length exhibited only a slight upward shift relative to the curve obtained with noise-free configurations. Since it is not possible to interpret all the results through a comparison of local positional information extracted from the stimulus configuration, we conclude that global information is also involved in the processing.

Discrimination, Psychological↗
PubMed1982

The development of map-reading skills.

The present study investigated the development of map-reading skills in kindergartners and second graders. The maps were read either inside or outside the space shown on the map, and they were either aligned with the space or rotated 90 degree or 180 degree. The current maps had only 1 landmark to establish the correspondence to the space. These impoverished maps allowed the examination of 2 variables not previously studied: the proximity of the target to the landmark (near vs. far) and the type of landmark (movable vs. fixed). Consistent with previous research, at both grades subjects were able to extract information from the maps to guide search. When the maps were rotated, the younger subjects made "egocentric" errors on the inside reading trials but not on the outside trials. At both grades, most errors preserved the near/far relation to the landmark. Thus, children extracted critical (near/far) information from the maps instead of creating a mental map which was then mentally projected in space.

Child↗
PubMed1998

Chlorophyll fluorescence analysis of cyanobacterial photosynthesis and acclimation.

Cyanobacteria are ecologically important photosynthetic prokaryotes that also serve as popular model organisms for studies of photosynthesis and gene regulation. Both molecular and ecological studies of cyanobacteria benefit from real-time information on photosynthesis and acclimation. Monitoring in vivo chlorophyll fluorescence can provide noninvasive measures of photosynthetic physiology in a wide range of cyanobacteria and cyanolichens and requires only small samples. Cyanobacterial fluorescence patterns are distinct from those of plants, because of key structural and functional properties of cyanobacteria. These include significant fluorescence emission from the light-harvesting phycobiliproteins; large and rapid changes in fluorescence yield (state transitions) which depend on metabolic and environmental conditions; and flexible, overlapping respiratory and photosynthetic electron transport chains. The fluorescence parameters FV/FM, FV'/FM',qp,qN, NPQ, and phiPS II were originally developed to extract information from the fluorescence signals of higher plants. In this review, we consider how the special properties of cyanobacteria can be accommodated and used to extract biologically useful information from cyanobacterial in vivo chlorophyll fluorescence signals. We describe how the pattern of fluorescence yield versus light intensity can be used to predict the acclimated light level for a cyanobacterial population, giving information valuable for both laboratory and field studies of acclimation processes. The size of the change in fluorescence yield during dark-to-light transitions can provide information on respiration and the iron status of the cyanobacteria. Finally, fluorescence parameters can be used to estimate the electron transport rate at the acclimated growth light intensity.

Acclimatization↗
PubMed2001

PIES, a protein interaction extraction system.

We consider the problem of extracting, manipulating, and managing biological pathways, especially protein-protein interaction pathways. We discuss here the Protein Interaction Extraction System (PIES). PIES is contructed on top of three main technologies: Kleisli, BioNLP, and Graphviz. Kleisli is a broad-scale data integration system that we use for downloading Medline abstracts and for general manipulation and management of pathway/interaction databases. BioNLP is a natural language-based information extraction module that we use for analysing Medline abstracts and to extract precise protein-protein and other interaction information. Graphviz is a graphical layout package developed for directed graphs that we use for visualization of the extracted pathways. PIES can be augmented with various means for extracting protein interaction information from sequence databases, for example, by using Kleisli's power to integrate sequence comparison tools to detect gene fusion events in sequence databases.

Abstracting and Indexing↗
PubMed2001

Event extraction from biomedical papers using a full parser.

We have designed and implemented an information extraction system using a full parser to investigate the plausibility of full analysis of text using general-purpose parser and grammar applied to biomedical domain. We partially solved the problems of full parsing of inefficiency, ambiguity, and low coverage by introducing the preprocessors, and proposed the use of modules that handles partial results of parsing for further improvement. Our approach makes it possible to modularize the system, so that the IE system as a whole becomes easy to be tuned to specific domains, and easy to be maintained and improved by incorporating various techniques of disambiguation, speed up, etc. In preliminary experiment, from 133 argument structures that should be extracted from 97 sentences, we obtained 23% uniquely and 24% with ambiguity. And 20% are extractable from not complete but partial results of full parsing.

Databases, Factual↗
PubMed2006

A water quality monitoring network design methodology for the selection of critical sampling points: Part I.

The principal instrument to temporally and spatially manage water resources is a water quality monitoring network. However, to date in most cases, there is a clear absence of a concise strategy or methodology for designing monitoring networks, especially when deciding upon the placement of sampling stations. Since water quality monitoring networks can be quite costly, it is very important to properly design the monitoring network so that maximum information extraction can be accomplished, which in turn is vital when informing decision-makers. This paper presents the development of a methodology for identifying the critical sampling locations within a watershed. Hence, it embodies the spatial component in the design of a water quality monitoring network by designating the critical stream locations that should ideally be sampled. For illustration purposes, the methodology focuses on a single contaminant, namely total phosphorus, and is applicable to small, upland, predominantly agricultural-forested watersheds. It takes a number of hydrologic, topographic, soils, vegetative, and land use factors into account. In addition, it includes an economic as well as logistical component in order to approximate the number of sampling points required for a given budget and to only consider the logistically accessible stream reaches in the analysis, respectively. The methodology utilizes a geographic information system (GIS), hydrologic simulation model, and fuzzy logic.

Environmental Monitoring↗
PubMed2001

Publishing web-based guidelines using interactive decision models.

Commonly used methods for guideline development and dissemination do not enable developers to tailor guidelines systematically to specific patient populations and update guidelines easily. We developed a web-based system, ALCHEMIST, that uses decision models and automatically creates evidence-based guidelines that can be disseminated, tailored and updated over the web. Our objective was to demonstrate the use of this system with clinical scenarios that provide challenges for guideline development. We used the ALCHEMIST system to develop guidelines for three clinical scenarios: (1) Chlamydia screening for adolescent women, (2) antiarrhythmic therapy for the prevention of sudden cardiac death; and (3) genetic testing for the BRCA breast-cancer mutation. ALCHEMIST uses information extracted directly from the decision model, combined with the additional information from the author of the decision model, to generate global guidelines. ALCHEMIST generated electronic web-based guidelines for each of the three scenarios. Using ALCHEMIST, we demonstrate that tailoring a guideline for a population at high-risk for Chlamydia changes the recommended policy for control of Chlamydia from contact tracing of reported cases to a population-based screening programme. We used ALCHEMIST to incorporate new evidence about the effectiveness of implantable cardioverter defibrillators (ICD) and demonstrate that the cost-effectiveness of use of ICDs improves from $74 400 per quality-adjusted life year (QALY) gained to $34 500 per QALY gained. Finally, we demonstrate how a clinician could use ALCHEMIST to incorporate a woman's utilities for relevant health states and thereby develop patient-specific recommendations for BRCA testing; the patient-specific recommendation improved quality-adjusted life expectancy by 37 days. The ALCHEMIST system enables guideline developers to publish both a guideline and an interactive decision model on the web. This web-based tool enables guideline developers to tailor guidelines systematically, to update guidelines easily, and to make the underlying evidence and analysis transparent for users.

Adolescent↗
PubMedDate not supplied

Accuracy of the oncology patients information system in a regional cancer centre.

This study was designed to evaluate the accuracy of the Oncology Patient Information Systems (OPIS) database for patients with breast cancer and lymphoma. We conducted a detailed individual patient chart review of patients with lymphoma or breast cancer who were seen in consultation by an oncologist between July 1991 and June 1995. Information extracted directly from the patients' clinic charts was compared with information captured in the OPIS database with respect to demographics, staging, histological diagnosis, treatment, relapse status, date of relapse and survival. OPIS database failed to capture 14.4% and 23.4% of lymphoma and breast cancer patients seen over the four-year period. When compared to the clinic charts there were differences in staging in 31.5% and 8.1%, relapse status in 27.6% and 7.2%, and date of relapse in 56.4% and 14.7% of lymphoma and breast cancer patients respectively. The deficiencies and inaccuracies in the OPIS database emphasize the need for caution in basing administrative, policy, or practice decisions on this database.

Breast Neoplasms↗
PubMed2005

Determination of the Fe content of embedded Cu-rich particles in ferritic alloys using energy-filtered TEM.

A novel technique for the quantification of the iron content of copper precipitates in ferritic steels is presented. Energy-filtered (EF) imaging has been used to extract elemental maps with high spatial resolution. These maps contain enough information to attempt the quantification of the signal produced by the precipitates when either a line profile is measured across them or the whole image signal is integrated. Assumptions such as sphericity of the precipitates and composition variations are discussed. Special attention to the assessment of drift on the information extracted from EF images has been taken. Minimum detectability and optimum acquisition conditions are discussed.

Journal Article↗
PubMedDate not supplied

Effects of battlefield display frames of reference on navigation tasks, spatial judgements, and change detection.

This paper describes an experiment which illustrates the cause of 'cognitive tunnelling' as it affects information gathering and perception-based task performance in computer-generated terrain displays of varying frames of reference. Cognitive tunnelling refers to the effect where observers focus attention on information from specific areas of a display to the exclusion of information presented outside these areas. Previous research suggests that cognitive tunnelling is induced by more immersive or egocentric visual displays. Results from our preceding study suggested that an immersed split-screen display induces cognitive tunnelling and results in poorer information extraction and situation awareness than an exocentric display of the same information. The current study determined that failure of the observers to integrate information across the two views of the immersed display led to the cognitive tunnelling effect. Cognitive tunnelling was also affected by primacy of information initially presented within the larger egocentric view in the immersed display.

Adult↗
PubMed2004

Phase differentiation via combined EBSD and XEDS.

Electron backscatter diffraction (EBSD) and orientation imaging microscopy have become established techniques for analysing the crystallographic microstructure of single and multiphase materials. In certain instances, however, it can be difficult and/or time intensive to differentiate phases within a material by crystallography alone. Traditionally a list of candidate phases is specified prior to data collection. The crystallographic information extracted from the diffraction patterns is then compared with the crystallographic information from these candidate phases, and a best-fit match is determined. Problems may arise when two phases have similar crystal structures. The phase differentiation process can be improved by collecting chemical information through X-ray energy-dispersive spectroscopy (XEDS) simultaneously with the crystallographic information through EBSD and then using the chemical information to pre-filter the crystallographic phase candidates. This technique improves both the overall speed of the data collection and the accuracy of the final characterization. Examples of this process and the limitations involved will be presented and discussed.

Copper↗